利用游离 DNA 中的甲基化特征进行敏感且特异的多癌种检测和定位。

BACKGROUND: Early cancer detection could identify tumors at a time when outcomes are superior and treatment is less morbid. This prospective case-control sub-study (from NCT02889978 and NCT03085888) assessed the performance of targeted methylation analysis of circulating cell-free DNA (cfDNA) to detect and localize multiple cancer types across all stages at high specificity. PARTICIPANTS AND METHODS: The 6689 participants [2482 cancer (>50 cancer types), 4207 non-cancer] were divided into training and validation sets. Plasma cfDNA underwent bisulfite sequencing targeting a panel of >100 000 informative methylation regions. A classifier was developed and validated for cancer detection and tissue of origin (TOO) localization. RESULTS: Performance was consistent in training and validation sets. In validation, specificity was 99.3% [95% confidence interval (CI): 98.3% to 99.8%; 0.7% false-positive rate (FPR)]. Stage I-III sensitivity was 67.3% (CI: 60.7% to 73.3%) in a pre-specified set of 12 cancer types (anus, bladder, colon/rectum, esophagus, head and neck, liver/bile-duct, lung, lymphoma, ovary, pancreas, plasma cell neoplasm, stomach), which account for ∼63% of US cancer deaths annually, and was 43.9% (CI: 39.4% to 48.5%) in all cancer types. Detection increased with increasing stage: in the pre-specified cancer types sensitivity was 39% (CI: 27% to 52%) in stage I, 69% (CI: 56% to 80%) in stage II, 83% (CI: 75% to 90%) in stage III, and 92% (CI: 86% to 96%) in stage IV. In all cancer types sensitivity was 18% (CI: 13% to 25%) in stage I, 43% (CI: 35% to 51%) in stage II, 81% (CI: 73% to 87%) in stage III, and 93% (CI: 87% to 96%) in stage IV. TOO was predicted in 96% of samples with cancer-like signal; of those, the TOO localization was accurate in 93%. CONCLUSIONS: cfDNA sequencing leveraging informative methylation patterns detected more than 50 cancer types across stages. Considering the potential value of early detection in deadly malignancies, further evaluation of this test is justified in prospective population-level studies.

背景：早期癌症检测可以在结果更好且治疗方式不太复杂的阶段发现肿瘤。这项来自 NCT02889978 和 NCT03085888 的前瞻性病例对照子研究评估了靶向分析循环游离 DNA（cfDNA）的甲基化以高特异性检测和定位多种癌症类型的表现。

参与者和方法：6689 名参与者[2482 名癌症（>50 种癌症类型），4207 名非癌症]分为训练集和验证集。血浆 cfDNA 进行了针对 >100000 个有意义的甲基化区域的亚硫酸氢盐测序。为癌症检测和组织起源（TOO）定位开发和验证了分类器。

结果：在训练集和验证集中表现一致。在验证集中，特异性为 99.3%[95%置信区间（CI）：98.3%至 99.8%；0.7%假阳性率（FPR）]。在指定的 12 种癌症类型（肛门、膀胱、结肠/直肠、食道、头颈部、肝脏/胆管、肺、淋巴瘤、卵巢、胰腺、浆细胞瘤、胃）的预定义集，I-III 期敏感性为 67.3%（CI：60.7%至 73.3%），占美国每年癌症死亡人数的约 63%，在所有癌症类型中的敏感性为 43.9%（CI：39.4%至 48.5%）。随着分期的增加，检测的敏感性也随之增加：在指定的癌症类型中，I 期的敏感性为 39%（CI：27%至 52%），II 期为 69%（CI：56%至 80%），III 期为 83%（CI：75%至 90%），IV 期为 92%（CI：86%至 96%）。在所有癌症类型中，I 期的敏感性为 18%（CI：13%至 25%），II 期为 43%（CI：35%至 51%），III 期为 81%（CI：73%至 87%），IV 期为 93%（CI：87%至 96%）。在具有癌症样信号的样本中，96%预测到了组织起源（TOO）；其中，93%的 TOO 定位准确。

结论：cfDNA 测序利用有意义的甲基化模式检测了 50 多种不同阶段的癌症。考虑到早期检测在致命性恶性肿瘤中的潜在价值，在前瞻性的人群水平研究中，进一步评估这种检测方法是合理的。